Various natural language processing (NLP) tasks necessitate deep models that are fast, efficient, and small based on their ultimate application at the edge or elsewhere. While significant investigation has furthered the efficiency and reduced the size of these models, reducing their downstream latency without significant trade-offs remains a difficult task....
This thesis addresses the problem of temporal action segmentation in videos, where the goal is to label every video frame with the appropriate action class present. We focus on the domain of NFL football videos, where action classes represent common football play types. For action segmentation, we use a temporal...
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A SNP resource for Douglas-fir: de novo transcriptome assembly and SNP detection and validation
Author(s): Howe, GT (Howe, Glenn T.)[ 1 ] ; Yu, JB (Yu, Jianbin)[ 1 ] ; Knaus, B (Knaus, Brian)[ 2 ] ; Cronn, R (Cronn, Richard)[ 2 ] ; Kolpak,...
This paper addresses the high model complexity and overconfident frame labeling of state-of-the-art (SOTA) action segmenters. Their complexity is typically justified by the need to sequentially refine action segmentation through multiple stages of a deep architecture. However, this multistage refinement does not take into account uncertainty of frame labeling predicted...
This study investigates the microstructure and mechanical properties of an austenitic Oxide Dispersion Strengthened (ODS) steel produced by the Laser Directed Energy Deposition (LDED) process using powder feedstock atomized with elemental yttrium. The Microstructure of the samples was characterized by electron microscopy, and mechanical properties were measured using a tensile...
The objective of this dissertation is to enhance the monitoring of forest ecosystems through the utilization of remotely sensed data to address the exigencies posed by the Anthropocene. On a global scale, rising temperatures and fluctuating precipitation patterns have strained forests and produced shifts in natural disturbance regimes. Additionally, the...
Robotic Bipedal locomotion holds the potential for efficient, robust traversal of difficult terrain. The difficulty lies in the dynamics of locomotion which complicate control and motion planning. Bipedal locomotion dynamics are dimensionally large problems, extremely nonlinear, and operate on the limits of actuator capabilities, which limit the performance of generic...
Within the past several years the technology of high-throughput sequencing has transformed the study of biology by offering unprecedented access to life's fundamental building block, DNA. With this transformation's potential a host of brand-new challenges have emerged, many of which lend themselves to being solved through computational methods. From de...
Pseudoperonospora cubensis is an obligate pathogen and
causative agent of cucurbit downy mildew. To help advance
our understanding of the pathogenicity of P. cubensis, we
used RNA-Seq to improve the quality of its reference
genome sequence. We also characterized the RNA-Seq
dataset to inventory transcript isoforms and infer alternative
splicing...
This honors undergraduate thesis examines the process of simulating power system state estimation, the use of the alternating direction method of multipliers in the problem of distributed power system state estimation, and provides a rudimentary asynchronous implementation of the above for a linearized DC power system. The asynchronous implementation is...
This study focuses on iodine-131 detected in milk samples from the Dairy Science Unit at Cal Poly, San Luis Obispo, California following events at the Fukushima Dai-ichi Nuclear Power Plant in March of 2011. The samples were collected as part of the Diablo Canyon Nuclear Power Plant (DCPP) Radiological Environmental...
Test case prioritization techniques schedule test cases for regression testing in an order that increases their ability to meet some performance goal. One performance goal, rate of fault detection, measures how quickly faults are detected within the testing process. The APFD metric had been proposed for measuring the rate of...
Nuclear fuel management is an optimization problem on many levels. Finding “viable” solutions for the core reload design problem is difficult without expert knowledge and software automation. Small modular reactors with a shared used fuel pool demonstrate a novel opportunity for fuel cycle optimization.
A Python package was developed and...
The development and some applications of holographic optical tweezers (HOT) are presented. Our HOT system uses a spatial light modulator (SLM) to control the location and properties of the optical trap. We have developed a method for optimizing the diffraction efficiency of a SLM that can be applied in situ...
Small modular reactors (SMRs) are a recent advancement in commercial nuclear reactor design with growing interest worldwide. New SMR concepts, such as the Multi-Application Small Light Water Reactor (MASLWR), must undergo a licensing processes established by the U.S. Nuclear Regulatory Commission (NRC) prior to commercial operation. Given the lack of...
7,7'-Dihydroxy-8,8'-biquinolyl (azaBINOL) was prepared from 7-hydroxyquinoline via N,N-dimethyl O-quinol-7-yl carbamate by directed ortho-metallation followed by FeCl₃-mediated oxidative coupling of the 8-lithioquinoline intermediate. Saponification of the resulting dicarbamate provided crystalline (±)-azaBINOL in 56% overall yield. 6,6'-Bis(dimethylaminocarbonyl)-7,7'-dihydroxy-8,8´-biquinolyl was prepared from the same dicarbamate by a double anionic-Fries rearrangement in 43% yield. 7,7'-Bis(diethylamino-carbonyloxy)-6,6'-diiodo-8,8´-biquinolyl...
This thesis describes an automated method to estimate tree trunk width in a commer-cial apple orchard. Trunk cross sectional area, which is an important consideration with regards to nutrient uptake, is a feature being integrated in a decision support system for precision Nitrogen management. The data used to generate the...
Top-performing approaches to embodied AI tasks like point-goal navigation often rely on training agents via reinforcement learning over tens of millions (or even billions) of experiential steps – learning neural agents that map directly from visual observations to actions. In this work, we question whether these extreme training durations are...
Detection of reactor antineutrinos for non-proliferation applications has been researched extensively across the globe and is considered as a potential technology to remotely monitor reactor operations without any intrusions to reactor components. Reactor antineutrino detection experiments have been conducted in the past and have proven successful in detecting the changes...
Many D2d-symmetric 2,2',6,6'-tetrasubstituted biphenyls are
readily prepared via net oxidative dimerization of appropriate
1,3-disubstituted benzenes. Conversion of such proprochiral
compounds to useful C2-symmetric chiral biphenyls requires
formal replacement of two substituents on opposing aryl ring
units with alternate groups. This under exploited
desymmetrization tactic has been demonstrated for the
generation...
This dissertation delves into understanding, characterizing, and addressing dataset shift in deep learning, a pervasive issue for deployed machine learning systems. Integral aspects of the problem are examined: We start with the use of counterfactual explanations in order to characterize the behavior of deep reinforcement learning agents in visual input...
Climate changes are growing environmental concerns which are much in the scientific government and public eye at present. The potential impact on aquatic resources and livelihood are immense. From local to global levels, fisheries and aquaculture play important roles for food supply, food security and income generation. Some 43.5 million...
Dysferlin is a ∼230 kDa terminally anchored membrane protein that is ubiquitously expressed, but is particularly enriched in skeletal and cardiac muscle tissue. Mutations covering the length of the protein have been linked to muscle wasting diseases including limb-girdle muscular dystrophy and Myoshi myopathy. Dysferlin has been shown to play...
As one of the most popular data types, the point cloud is widely used in various appli- cations, including computer vision, computer graphics and robotics. The capability to directly measure 3D point clouds is invaluable in those applications as depth information could remove a lot of the segmentation ambiguities in...
In order to address the energy needs of developing countries and remote communities, Oregon State University has proposed the Multi-Application Small Light Water Reactor (MASLWR) design. In order to achieve five years of operation without refueling, use of 8% enriched fuel is necessary.
This dissertation is focused on core design...
Over time, Open Source Software (OSS) has become indispensable in the creation and upkeep of software products, serving as the fundamental building block for widely used solutions in our daily lives, including applications that enable communication, entertainment, and productivity. A sustainable OSS ecosystem is one that attracts and retains a...
With the strong shift toward network-centric cluster-computing workload management has become increasingly important in both industrial and academic environments. To fully harness the distributed computing resources of the 32 PC's in our department, I developed a workload monitoring system together with a few utilities for users to submit either sequential...
Understanding and modeling microbial responses and feedbacks to climate change is hampered by a lack of a framework in the pelagic environment by which to link local mechanism to large scale patterns. Where terrestrial ecology draws from landscape theory and practice to address issues of scale, the pelagic seascape concept...
Animals aggregate and interact in nonuniform and nonrandom patterns, which lead to group level characteristics that have important evolutionary and ecological consequences. Network analysis provides a useful conceptual framework for linking animal interactions at all scales from dyads to communities, to populations and ecosystems. Despite exciting theoretical and applied advances...
Geographical datasets are large, complex, and can be difficult for users to navigate and derive meaning from. These datasets, as well as the unique insights derived from them, provide tremendous opportunity for social change -- many of the global challenges humankind is currently facing can benefit from analytics or visualization...
RNA silencing pathways are required for a wide variety of processes in most
eucaryotes. In plants, small-interfering RNA (siRNA) arising from transposons and other
repetitive sequences is associated with heterochromatin formation and maintenance.
MicroRNAs and trans-acting siRNAs encoded at discrete loci function as negative regulators of
gene expression by triggering...
Marine sediments are vast sources and reservoirs of methane, a potent greenhouse gas. Most of this methane is anaerobically oxidized by archaea before it can reach the overlying ocean, though the efficiency of this process often depends on methane fluxes and mechanisms of fluid transport. Anaerobic methanotrophic archaea, or ANME,...
This thesis uses a hedonic price model to estimate the value of water for irrigation in Deschutes County, Oregon. The analysis uses a dataset comprising information on 2,274 agricultural parcels across the County. Uniquely, the analysis successfully utilizes assessor-determined real market values in the place of actual land sales. A...
Regression testing is an expensive testing process used to validate changes made to previously tested software. Different regression testing techniques can have different impacts on the cost-effectiveness of testing. This cost-effectiveness can also vary with different characteristics of test suites. One such characteristic, test suite granularity, reflects the way in...
The elimination of soluble boron creates several advantages for Small Modular Reactor (SMR) operation. Most of these advantages are realized through significant core simplification (removal of pipes, pumping, and purification systems), the removal of the corrosive effects of soluble boron, and from improved safety effects. However, removing soluble boron creates...
This work is a culmination of a series of published works related to the use of the Material Point Method (MPM) in modeling wood adhesive bonds. The use of wood as construction material has the potential to play a small role in the solution to the current CO2 and climate...
Detection technique that proposed utilizing electrochemically controlled, reversible ion extraction into polymeric membrane in an alternating galvanostatic/ potentiostatic mode was introduced. This method is studied in detail to comprehend the advantages of the novel sensor (pulstrode) compared to the potentiometric ion selective electrode (ISE), studies included possible applications and limitations....
How can rigorous forms of testing be supported in a way that is both compatible with the visual aspect of visual programming languages, and usable by the audiences using those languages - even when the audience has no background in software engineering? Visual programs are likely to contain at least...
Papain-like leader proteases are found in diverse families of human, animal, plant, and fungal positive-strand RNA viruses. In addition to autocatalytic processing, these proteases play a variety of roles in the virus life cycle. In particular, the leader protease (L-Pro) of a prototype member of the Closterovirus genus, Beet yellows...
Beet yellows virus (BYV) is a filamentous, positive-strand RNA virus that belongs to the family Closteroviridae. BYV particles encapsidate a 15.5 kb RNA and posses complex polar architecture. A long virion body is formed by the major capsid protein(CP), whereas the minor capsid protein (CPm) assembles a short tail that...
At a time when the biodiversity on Earth is being rapidly lost, new technologies and methods in genomic analysis are fortunately allowing scientists to catalog and explore the diversity that remains more efficiently and precisely. The studies in this dissertation investigate genomic diversity within the milkweed genus, Asclepias, at multiple...
European hazelnut (Corylus avellana L.) is an important crop Oregon's Willamette Valley, producing 99% of the hazelnuts grown in North America and brings over US $60 million dollars to the region annually. Hazelnuts are rich in fiber and vitamins, as well in demand by consumers due to their popularity as...
Global electromagnetic (EM) induction studies have been the focus of increasing attention during the past few years. A primary stimulus for this interest has been increased quality, coverage and variety of the newly available data sets especially from recent low-Earth-orbiting satellite missions. The combination of traditional ground-based data with satellite-borne...
The use of board games for teaching introductory computer science is a promising recent avenue of research. The goal is to introduce computing concepts through their use in the implementations of simple games, thereby keeping students engaged through their learning process. However, there is a gap between students' algorithmic descriptions...
State-of-the-art personal robots need to perform complex manipulation tasks to be viable in complex scenarios. However, many of these robots, like the PR2, use manipulators with high degrees of freedom. High degrees of freedom are desirable from a functionality standpoint, but make the learning task more difficult by adding a...
This thesis seeks to determine whether a self-driving car's behavior should depend on the hearing status of its passengers: namely, hard-of-hearing (including deaf) or hearing. It is believed that auditory deprivation provokes adaptations in visual attention. These adaptations may lead to atypical movement patterns that can translate to different driving...
In this dissertation, we propose Ideal Thumbnail-Preserving Encryption (Ideal TPE), as a special case of format-preserving encryption, to balance image privacy and usability concerns in a cloud environment. We first introduce a concrete construction for Ideal TPE, that provably leaks nothing about the plaintext (unencrypted) image beyond its thumbnail. We...
Programming parallel machines has been a difficult and unrewarding task. The short lifespan of parallel machines and their incompatibility have made it difficult to utilize them. Our goal here is to create an environment for parallel computing which allows users to take advantage of parallel computers without writing parallel programs....
Pathogen invasions pose a growing threat to ecosystem stability and public health. Guidelines for the timing and spatial extent of control measures for pathogen invasions are currently limited, however. We conducted a field experiment using wheat (Triticum aestivum) stripe rust, caused by the wind-dispersed fungus Puccinia striiformis, to study the...
The Line Integral Convolution (LIC) is a mainstay of flow visualization. It is, however, computationally intensive, which limits its interactivity. Also, when used to view three-dimensional (3D) vector fields, the resulting images are dense and cluttered, making it difficult to perceive the flow on the interior parts of the field....
In its simplest form, the process of diagnosis is a decision-making process in which the diagnostician performs a sequence of tests culminating in a diagnostic decision. For example, a physician might perform a series of simple measurements (body tem- perature, weight, etc.) and laboratory measurements (white blood count, CT scan,...
Studies of light-matter interactions in organic semiconductors and in optical tweezer trapping of nanoparticles are presented. In the research related to organic semiconductor materials, a variety of novel materials and their composites have been characterized, and physical mechanisms behind their optoelectronic properties have been established. Three novel functionalized hexacene derivatives...
Solid state luminescent sulfides are prepared as powders in order to elucidate the relationship between structure and light emission. While the sulfides studied in this dissertation are known phosphors, materials are investigated in a variety of new ways. Elementary properties and structures of MgS are reviewed, and preparation of MgS...
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I understand that my dissertation will become part of the
The development of micro total analysis systems (µTAS), also called “lab-on-a-chip”, or microfluidic analysis systems, is presented in this dissertation. Various research areas, covering subjects from magnetic particles synthesis to novel microchip fabrication techniques, are explored to develop a lab-on-a-chip system capable of performing magnetic bead-based bioassays. These devices are...
The well-known fact that tropical sea level can be usefully simulated by linear wind driven models recommends it as a realistic test problem for data assimilation schemes. Here we report on an assimilation of monthly data for the period 1975-1992 from 34 tropical Pacific tide gauges into such a model...
NCRP report No.160 states that medical exposure increased to nearly half of the total radiation exposure of the U.S. population from all sources in 2006 (NCRP 2009). Part of this increase in exposure is due to the rise in nuclear medicine procedures. With this observed growth in medical radionuclide usage,...
How should reinforcement learning (RL) agents explain themselves to humans not trained in AI? To gain insights into this question, we conducted a 124 participant, four-treatment experiment to compare participants’ mental models of an RL agent in the context of a simple Real-Time Strategy (RTS) game. The four treatments isolated...
Deep neural networks currently comprise the backbone of many applications where safety is a critical concern, for example: autonomous driving and medical diagnostics. Unfortunately these systems currently fail to detect out-of-distribution (OOD) inputs and can be prone to making dangerous errors when exposed to them. In addition, these same systems...
We have developed a compact micro total analysis system (μTAS) to serve as a platform for in-situ spectrophotometric water quality monitoring. Individual fluidic, optical, and electrical components were designed, developed, and characterized. These components were combined in both an integrated (single lithographic “chip-based” platform) and a modular manner. The microfluidic...
Plant diseases often cause serious yield losses in agriculture. A pathogen’s invasiveness can be quantified by the basic reproductive number, R₀. Since pathogen transmission between host plants depends on the spatial separation between them, R₀ is strongly influenced by the spatial scale of the host distribution.We present a proof of...
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distribution
Alexey MIkAberIdze,1,3 chrIstopher c. Mundt,2 And sebAstIAn bonhoeffer1
1Institute of
Plant diseases often cause serious yield losses in agriculture. A pathogen’s invasiveness can be quantified by the basic reproductive number, R₀. Since pathogen transmission between host plants depends on the spatial separation between them, R₀ is strongly influenced by the spatial scale of the host distribution.We present a proof of...
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A. Mikaberidze et al.
Alexey Mikaberidze, Christopher C
The purpose of this thesis is to design a robust test facility for a small space nuclear power system and model its physical behavior under different scenarios. The test facility will be used to simulate a 1-10kWe nuclear reactor, its electrical generation, and heat removal capabilities. This simulator will be...
PDMS membrane-based microvalves are becoming increasingly more important for the control of fluid flow within MECS applications such as microreactors used to synthesize nanoparticles and biological macromolecules. The motivation for pursuing PDMS membrane-based microvalves is for implementing a plug flow microreactor to simulate slug flow yielding a narrower residence time...
As the semiconductor industry works to integrate increasingly more "non-CMOS" devices onto CMOS ICs, compact model development has become an important step in the circuit/system verification tool flow. This research focuses on the two- and three-dimensional modeling of the physical phenomena that occur in nanoscale magnetic devices. This includes the...
A transient code (TFETC) for calculating the temperature
distribution throughout the radial and axial positions of a
thermionic fuel element (TFE) has been successfully developed.
It accommodates the variations of temperatures, thermal power,
electrical power, voltage, and current density throughout the
TFE as a function of time as well as...
Wildtype sunflower typically produces 12-24% oleic acid (18:1) and 70-82%
linoleic acid (18:2). High-oleic sunflower, by contrast, produces up to 80-94% oleic
acid. The monounsaturated oleic acid has a greater oxidative stability than the
polyunsaturated linoleic acid, predominant in wildtype sunflower, and has greater
nutritional benefits than polyunsaturated and saturated...
Gamma Ray Bursts (GRBs) are the most energetic explosions in the Universe, producing up to $\sim10^{53}$ ergs of energy in the first few seconds of their emission -- the so-called prompt phase that is dominated by high energy X-ray and $\gamma$-ray photons. The very large luminosities released in these events...
The recent 2013 Oregon State Board of Agriculture report identified several ways to improve agricultural income in Oregon. Recommendations to improve water development are at the top of the report's list of objectives. In this study, I analyze the relationship between net cash farm income (NCFI) and a cross-sectional set...
The Open Modeling Environment (OME) is a tool developed to address some known shortcomings in ecological System Dynamics (SD) modeling research. OME provides a common set of methods for interacting directly with spatial information, reducing the need for modelers to create their own methods for doing so. The environment is...
In open set recognition, a classifier must label instances of known classes while detecting instances of unknown classes not encountered during training. To detect unknown classes while still generalizing to new instances of existing classes, this thesis introduces a dataset augmentation technique called counterfactual image generation. This approach, based on...
Successful software systems evolve over their lifetimes through the cumulative changes made by software maintainers. As software evolves, the problems resulting from software change worsen, exacerbated by increased system size and complexity, lack of program understanding, amount of effort required to make changes, and number of personnel involved. Experience shows...
Chemical synthesis of oligonucleotides is a widely used tool in the field of biochemistry.
Several methods for gene synthesis have been introduced in the growing area of genomics.
In this paper, a novel method of constructing dsDNA is proposed. Short (28-mer) oligo fragments
from a library were assembled through successive...
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. doi: 10.1038/nmeth.2918 PMID: 24781323
3. Borodina TA, Lehrach H, Soldatov AV. Ligation-based
Adjoint-derived weight windowing is a hybrid deterministic/Monte Carlo method to simulate radiation transport. In adjoint-derived weight windowing, a deterministic adjoint solution is used to create weight windows for a Monte Carlo simulation. The intent of this work is to identify factors that reduce the Figure of Merit (FOM) of Monte...
This dissertation addresses the problem of video labeling at both the frame and pixel levels using deep learning. For pixel-level video labeling, we have studied two problems: i) Spatiotemporal video segmentation and ii) Boundary detection and boundary flow estimation. For the problem of spatiotemporal video segmentation, we have developed recurrent...
A novel method for detecting the peptidase activity of clinically relevant peptidases was investigated using solid-contact electrochemical polyion sensors under chronopotentiometric control. Complete instrumental control over ion-extraction was accomplished by incorporating a lipophilic electrolyte into the ion-selective membrane; the sensors had no intrinsic ion-exchange capabilities. The sensors were used to...
Ion-selective polymeric optical sensors – ion optodes – are a promising alternative to ion-selective electrodes and fluorescent dyes for analytical and biological applications, e.g. extra- and intracellular measurements. They are non-toxic, highly selective robust probes for ionic fluxes monitoring.
A large-scale fabrication of ion optodes using a solvent displacement method...